Ash's Orre Journey
by RonnyBravo the Breadghost
Summary: Immediately upon arrival back in Pallet Town after the Unova League, Ash finds himself whisked away on another journey, this time to Orre, at the request of Professor Krane to help investigate the Shadow Pokémon crisis. Though excited at first, he soon realizes what a critical matter this incident is...
1. A New Beginning

Chapter 1: A New Beginning

The breeze whisked through Ash's hair as he dashed towards the Professor Oak Pokémon laboratory. Coming off of a loss in the finals in the Unova league, he was excited to get home and release all of the Pokémon he got in Unova into Professor Oak's laboratory, and interested to see how they would get along with Pokémon he had caught in other regions. They had all been kept at Professor Juniper's lab in Unova until he picked them up before he grabbed the plane for Kanto.

Now here he was, running along the path, and he said as Professor Oak's laboratory came into view, "There it is Pikachu! We're finally home!" He hadn't gone straight home because while he was on the plane, one of the flight attendants had told him that his mother called and told him to go straight to the lab. He was fine with that, especially carting nine Poké Balls with him.

He pushed up the steps as he reached them and ran straight up to the door. He rang the doorbell and Tracey answered it.

"Ash! It's been so long!" he exclaimed.

"It sure has," he said, "Where is everybody?"

"They're all out back," said Tracey, "Follow me!" Ash walked inside with Tracey and shut the door behind him. He felt the four extra Poké Balls on his belt expand, signifying that he was on home turf and could release all of his Pokémon at once. Tracey escorted him outside and Ash was met with a huge assembly of Pokémon as he exited the building. They all ran up to greet him.

"Welcome home Ash!" his mother and Professor Oak exclaimed.

"Thanks," said Ash as he bent down to greet the smaller Pokémon. All of his Pokémon from his past adventures were there, from Bulbasaur to Gible. As he and Pikachu greeted them all happily, he remembered that he had his Unova Pokémon at his fingertips. He got up and reached for the nine Poké Balls at his belt and threw them in the air one by one.

"Come on out guys!" he called as the Poké Balls opened up.

His nine Unova Pokémon came out of their Poké Balls one by one, and each of them, from Unfezant to Krookodile stood before the large congregation of Ash's older Pokémon.

"That's quite a crowd," said Delia Ketchum.

"It sure is," said Ash, "They're all really awesome friends." The older Pokémon stared at the newer, some with different reactions. Staraptor seemed to take particular interest in Unfezant for example, and Totodile and Oshawott were observing each other quizzically. The others simply got caught up in conversation with Ash's older Pokémon.

"They seem to be getting along," said Ash.

"Well that's typical," said Professor Oak, "They were all raised by you and have had your influence."

"Why don't we go inside for tea?" asked Tracey. Everyone agreed and left the Pokémon to their conversation as they went inside.

* * *

As they sat down in the living room, a Buizel jumped up onto the couch and began sniffing around Ash inquisitively. Then it looked up at him and tilted its head to the side.

"This isn't my Buizel is it?" asked Ash in confusion as to why the Pokémon had taken such a sudden interest in him.

"Of course not," said Professor Oak, "That's another Buizel from here in the garden that we call Bui."

"Wow, you have name for him?" asked Ash.

"It wasn't our idea," said Tracey, "It was your Buizel's idea." Right on cue, Ash's Buizel jumped up from behind the couch and then down on the cushions next to the other Buizel.

"So you've taken to this little guy huh?" Ash asked Buizel. The younger Buizel had embraced his own and hidden behind him, in sudden fear of Ash's presence. Pikachu jumped down to say hello.

"Well Ash, you catch on quickly," said Professor Oak as the Pokémon conversed, "Your Buizel and that Buizel have had such a parent-child relationship since we first discovered the younger one and his sister in the garden. As a matter of fact, from so much observation, we think that this young Buizel could very well be your Buizel's child."

"Cool!" said Ash, oblivious to the last statement that Professor Oak had stated, "So you're taking care of the little ones now!" Buizel seemed confused at Ash and then patted the Buizel who was presumably his son on the back so as to tell him to go out of the lab. The young Buizel nodded and waved at Pikachu before departing through the open window.

"So you placed second in the Unova League!" Delia exclaimed, restarting the conversation, "That is higher than you've ever gotten right?"

"Yep," said Ash, "Before that, the farthest I'd gotten was the semi-finals in Sinnoh. That was a hard battle."

"You weren't up against legendary Pokémon this time though," said Professor Oak, "That might have been a contributing factor."

"Nah," said Ash, "I think our skill and power went through the roof of that place!" They all laughed heartily.

"Well then, what are you going to do now that you're done in Unova?" asked Tracey. Ash thought for a few moments.

"I might stay home for a while," he said as Pikachu jumped onto his shoulder, "I never stay home for longer periods of time."

"Oh Ash, it's quiet without you here," said Delia teasingly, "I think it'd be nice if you went off on another journey."

"Mom…" said Ash.

"I'm just kidding," said Delia. Muk suddenly came up from behind the seat Professor Oak was sitting in and swamped him.

"Aughh!" Professor Oak cried, "Muk!" Everyone laughed at Muk's usual antics when something suddenly came to Ash's mind.

"Hey, I just realized that I've never travelled with Muk," said Ash, "Maybe I should take her along the next time I go on a journey." Muk swamped Professor Oak even more in order to get over to Ash in excitement. She tumbled off of Professor Oak and onto the floor and proceeded to go under the coffee table and climb onto the couch next to Ash in order to hug him. Pikachu jumped off of his shoulder and onto the arm of the couch.

"Hey!" Ash cried as she swamped him, "Yeah, I know you like me! Get off!" Muk tumbled back onto the floor.

"Well it seems Muk likes the idea," said Tracey.

"Most certainly," said Delia.

"Yes, I think that would be a weight off of my shoulders," said Professor Oak, still trying to recover from the most recent Muk attack, "Quite literally. It gets old having Muk try to strangle me all the time."

"Well she does really like humans," said Tracey.

"I know that, but I'm just saying," said Professor Oak. The phone suddenly rang from the next room.

"I'll get it!" said Tracey before anyone else could get up. He ran into the next room and the others in the room waited for him to get back. A few minutes later, he came back and said in a serious tone, "Professor, it's for you." Professor Oak got up and walked into the next room. Not five seconds later he called, "Ash, can you come here?" Ash hesitated before getting up, Pikachu back on his shoulder and Muk and his mother following him.

As he entered the room, he saw a man with brown hair and glasses on the screen of the phone. The man wore a labcoat.

"Ah, hello," said the man on the screen, "You must be Ash."

"Yeah, that's me," said Ash.

"Ash, this is Professor Krane from the Orre region," said Professor Oak, "He does research on how to help Pokémon with their problems."

"Now Oak, we don't have to conceal anything," said Professor Krane, "What I really study is Shadow Pokémon."

"Shadow Pokémon," said Ash, contemplating the idea, "What are those?"

"Shadow Pokémon are Pokémon that have been turned into fighting machines by people, having their hearts closed to the world," said Professor Krane, "They were a particular threat in the Orre Region five years ago. My old friend and I were studying how to open their hearts in an easier manner before he died. Then they showed up again just last week, under the influence of the same organization that had turned them into Shadow Pokémon in the first place. We need the help of some strong trainers to find out exactly what is going on."

"I'd be happy to help," said Ash.

"Excellent," said Professor Krane, "You better hurry though. I sent a note to the captain of the S. S. Libra, which is leaving from Kanto at three o' clock. I'll look forward to your arrival." The screen went blank.

"Well, I guess you'll be going on another journey after all," said Delia.

"Yep," said Ash, "And Muk will get to come along as well!" Muk tackled him in glee and everyone laughed.

* * *

The salty ocean breeze blew past Ash as he looked over the sea from the deck of the Libra. It was now four o' clock, and they were certainly enjoying the start of this new journey.

"This is great," said Ash, stretching his limbs, "Soon we'll be in the Orre region!" The first mate came up beside him.

"Not for a while actually," he said, "We won't be arriving until tomorrow morning."

"I know, but it's exciting," said Ash. Muk swamped him for the third time since the start of the trip, and Pikachu landed on the deck next to the two of them. The first mate laughed heartily.

"You seem to be really close to your Pokémon Ash," he said.

"Yeah…" said Ash from underneath Muk, "I really am aren't I…"

* * *

That night, Ash was unable to sleep. Pikachu was snoring on his chest, while Muk resided under the bed. Ash himself stared at the ceiling, excited for what might happen in Orre. He still had questions about this whole Shadow Pokémon idea, and he wanted to ask them to Professor Krane as soon as he got to Orre.

He began to doze off, and when his mind became clear again, the darkness was still around him. Then he heard something from outside. He sat up and Pikachu awakened from his deep slumber.

"You hear that Pikachu?" Ash asked. Muk was up now too, and Ash had gotten up to look out of his cabin's window. It was the only open space, since most of the rest of the ship had Pokémon being transported to Orre on it. He looked out and up and heard the sound more clearly; it was the sound of helicopter blades turning quickly.

Ash and his two Pokémon looked up in shock as they saw three helicopters train their searchlights on the ship. Then, another dark figure formed in the night above them. Ash couldn't tell what it was exactly, as it was so dark, but it looked downright evil. He heard the scream of a Pokémon, and suddenly, a huge purplish light pierced into the ship. Ash, Pikachu, and Muk were all thrown to the ground. Ash felt the ship being lifted up, swaying back and forth. He quickly stood up and shut the window so none of them would fly out. Then he was thrown to the ground again, and he hit the bed with his head, and was knocked unconscious.

* * *

**A/N: Yes, I know it is a very childish and short beginning, but don't we all agree that this is how most of the anime series started? Ash becoming obligated to go to another reason for whatever reason, usually to beat its Pokémon league (or to deliver the GS Ball)? Yeah, I thought so. I started writing this story long before the Unova League so the conversation at the beginning skews the timeline, but that's alright. This story will get more serious and less childish as I go along (I hope) but Ash will be Ash (although we will see some of his more interesting traits come out through the course of this story). And I am deliberately publishing this on the exact day I joined fanfiction 2 years ago, simply because I can. :D**

**I do not own Pokémon, it belongs to GameFreak and Nintendo. **


	2. The Ship in the Desert

Chapter 2: The Ship in the Desert

When Ash awoke again, he found Pikachu and Muk looking down upon him. Bright light streamed into the window now. Ash blinked a few times before sitting up and finding himself lying on the floor next to the bed.

"What happened?" he asked groggily. The back of his head hurt, which meant it all hadn't been a dream. Deciding to investigate, Ash dressed himself and grabbed his hat, and he and his two Pokémon walked out of the cabin.

* * *

"Captain!" he called, "Captain!" He was searching the interior of the ship. Numerous Pokémon were cowering behind boxes and machine parts as he walked around. He was perplexed as to what might have happened. Eventually, he found himself on the deck of the ship again, and was shocked at what he saw. The ship was in the middle of a desert now, and large parts of it were broken off and lying in the sand around the main body.

"What happened?" Ash asked himself. Suddenly, he heard voices.

"Is the next transport ready?" he heard someone ask.

"Just a few more Pokémon and it should be," came the answer. Two men dressed in strange white outfits and wearing red bandanas walked around the side of the ship. White helmets covered their faces. Ash, Pikachu, and Muk all ducked behind some boxes that were nearby and listened in.

"One last inspection," one of them said, throwing a Poké Ball into the air. A white light flashed, and a Poochyena came out.

"Sniff around Poochyena," the trainer ordered. The Poochyena immediately set its nose to the ground and began sniffing; right towards Ash.

"Here it comes," said Ash, holding his breath, "Pikachu, if it gets too close, use Thunderbolt!" Pikachu nodded, just as the Poochyena turned the corner of the boxes. It lifted its head, growled in a feral tone, and charged directly at them. Pikachu zapped.

Immediately, the two men ran over, releasing three more Pokémon between them. They were a Ninjask, Ledyba, and Voltorb. The Poochyena ran back to its owner as though it hadn't been hit. Ash stood up, realizing he had been discovered, and prepared for a battle.

"Who are you?" he asked the two men.

"You don't need to know that kid," said the one with the Voltorb and Poochyena, "Voltorb, use Spark, and Poochyena, Shadow Blitz!" The two Pokémon charged their respective attacks and attacked.

"Muk, use Protect!" Ash yelled swiftly. Muk got in front of her teammates and put up a green wall of light.

"Dang it!" the other grunt yelled as the attacks bounced off, "Ninjask, Fury Cutter, and Ledyba, use Shadow Blitz!" Ninjask shot forward at lightning speed, but Pikachu zapped it with Thunderbolt, while Muk swamped the Ledyba.

Ash was quite confused as this was going on. Whereas the Voltorb and Ninjask seemed to be tiring, the other two, the Ledyba and Poochyena, didn't seem to be affected at all. They had also used attacks Ash had never seen before.

"Pikachu, use Electro Ball, and Muk, use Sludge Bomb!" Ash ordered. Pikachu charged his attack and fired a ball of yellow electrical energy, while Muk opened her mouth wide and fired a few shots of poison at their opponents. The attacks made direct contact, and the Ninjask and Voltorb were knocked out, but the Poochyena and Ledyba still seemed unfazed.

The two of them returned their fainted Pokémon and gritted their teeth.

"Stupid kid!" they yelled in unison, "Get them!" A double Shadow Blitz flew at Ash but Muk blocked the blow with Protect. The two abnormal Pokémon were thrown back, but still seemed unfazed.

"Pikachu, one last time, use Thunderbolt!" Ash yelled. Pikachu charged his electrical energy and fired a blast of electricity at the two Pokémon. They finally wobbled and fell over. The two men showed a look of panic on their faces.

"What do we do?" the first one asked the second.

"I don't know…" said the second one, "We'll have to send in more troops later. I'm sure the boss will understand." With that, they ran towards the edge of the ship and jumped off. Ash ran to the edge in shock and watched them get into a strange vehicle, which propelled itself across the sand, vanishing in the distance within seconds.

Ash turned to the two Pokémon they had left behind. He walked up to them and bent down to pet them, but they suddenly jumped up and the Poochyena snapped at him.

"Hey, I'm trying to help you!" Ash cried. The Poochyena had none of his words and ran off, disappearing into the ship. The Ledyba tackled Ash to the ground and then made an attempt to fly off.

"Muk, use Sludge Bomb!" Ash called. Muk opened its mouth and shot the Ledyba out of the air with a single blast of poison. The little Pokémon fell to the ground and tried to fly off again, but Ash picked it up. It head-butted him multiple times, but he didn't let go.

"What is wrong with you?" Ash asked pleadingly. The Ledyba wouldn't stop attacking him. Finally, Ash dropped it and it fell to the ground again. It tried to fly off, but it couldn't. Ash fell to his knees from all of the hits he had just taken. The Ledyba collapsed from exhaustion. Ash pulled out a Poké Ball from his belt.

"Hey Ledyba, you're hurt," he said, "Why don't you come with me and I'll get you something to heal you." The Ledyba turned around to him and glared at him with a feral stare. It charged at him enveloped in a shadowy aura, just as it had when the men had commanded it to Shadow Blitz before, but Ash threw the Poké Ball before it could reach him. To his utmost shock, the Poké Ball opened, and the Ledyba went inside. After a few seconds, the Poké Ball snapped shut and Ash picked it up off of the ground.

"What's going on around here?" he asked himself.

* * *

After searching through the ship numerous times, he found that there was an exit that had been ripped in the hull. He could see the tracks of many Pokémon in the sand around the ship, which must have meant that many of the ones on the ship had run off. He was saddened to think that they were lost in the desert somewhere. Of course, those guys had talked about some sort of transport… perhaps they had been trying to rescue the Pokémon.

"No," Ash said to himself, looking at Ledyba's Poké Ball, "Anyone who has a Pokémon like this can't possibly care about Pokémon." Something was wrong with the Ledyba. Ash couldn't connect with it somehow. He knew because his Aura, which had aided him many times, could not comprehend the Aura around the Ledyba. He wondered if it was one of the Shadow Pokémon that Professor Krane had been talking about.

"I wonder where we are," said Ash, "And what happened to the crew." Pikachu's ears drooped in the heat, and Ash returned Muk to her Poké Ball so that she wouldn't get sand all over her. He didn't stray far from the ship, but that was the least of his worries. Out of nowhere, a sandstorm began brewing around him.

"Darn it!" he yelled, getting sand in his mouth. He fell to the ground and the sand beat him down to unconsciousness.

* * *

When Ash woke up again, he found himself lying on a soft bench staring up at the ceiling of some sort of engine. He checked is belt, and found that the two Poké Ball enclosed Pokémon were still there. Then he sat up with a start and looked around.

"Where am I?" he asked in panic.

"The Outskirt Stand," said a voice on the opposite side from where he was sitting. Ash looked over. He was sitting at a table inside an old fashioned steam engine car. A jukebox played low and jazzy tunes. Pikachu was standing on the table next to a man with purple spiky hair. Pikachu jumped onto his shoulder.

"Pikachu!" Ash exclaimed, "Are you alright?" Pikachu responded happily.

"Great," said Ash jovially. Then he turned to the man. "Thanks for saving us," he said.

"No problem," said the man, "The name's Willie. You seemed pretty wiped out walking out there alone in the desert. I wouldn't think anyone would risk going out in a sandstorm like that, much less go that far out in the first place."

"Then why were you out there?" asked Ash.

"The Outskirt Stand is only about a mile or two from where I found you," Willie said, scratching the back of his head, "I practically live here. What were you doing out in the desert?"

"Well, you see…" Ash started. He told Willie what had happened with the S.S. Libra. Willie nodded along to the short story.

"So that's what that was…" he said, "People claimed to have seen something enormous flying across Orre last night. Someone even thought it was a flying Wailord."

"That must have been the Libra," said Ash. Willie nodded.

"And you say you were supposed to meet Professor Krane at the HQ Lab in the north, eh?" said Willie.

"Of course," said Ash. Willie grinned.

"Alright, I'll take you there," he said, "But not until you have a battle with me." Ash stood up.

"You're on!" Ash exclaimed, Pikachu mirroring his movements. Willie stood up.

"Let's go outside then," he said. He walked out and Ash followed.

Just outside the Outskirt Stand was what appeared to be train wreckage in the middle of the desert. There was nothing around for miles but sand, and broken axles and wheels lied around everywhere.

Willie picked two Poké Balls from his belt.

"I should probably explain to you this Ash," he said with a mischievous smile, "Everyone you battle here in Orre will ask for a double battle and nothing else. It's just the way we do things." Ash nodded.

"Alright then," he said reaching for his belt. He wanted to use Ledyba, but when he touched the Poké Ball, it shook violently and then stopped. Ash moved his hand over hesitantly as he realized again that Ledyba seemed to really not like him. He grabbed Muk's Poké Ball and held it up.

"I'm ready," said Ash confidently.

"That's what I like to hear," said Willie, "Zigzagoon and Linoone, you're up!" The two Poké Balls were thrown and both Pokémon flew out in a flash of blue light. They waited patiently as Ash called out his two.

"Muk, Pikachu, I choose you!" he yelled, throwing Muk's Poké Ball as Pikachu jumped off of his shoulder. Muk appeared next to Pikachu and the battle began.


	3. Drussel City

Chapter 3: Drussel City

"Double Quick Attack!" Willie said immediately. Zigzagoon and Linoone both shot forward at once, shooting directly at Pikachu.

"Muk, get in front of Pikachu and use Protect!" Ash yelled. Muk did so. Both of the opposing Pokémon were thrown backwards and skidded back to their starting positions.

"Nice move," Willie commented.

"We're just getting started!" Ash exclaimed, "Pikachu, use Thunderbolt!" Pikachu shot a blast of electricity straight at the opponents.

"Linoone, Safeguard!" Willie called. A large sphere of green light surrounded both it and the Zigzagoon. The Thunderbolt bounced off with no effect.

"How long will this battle of shields last?" Willie asked in an almost taunting manner. Ash responded with another command.

"Muk, get in close and use Sludge Wave!" Ash yelled. Muk moved in charging the attack, but by the time it was close enough to attack, the opposing Pokémon were already out of the way, behind Muk.

"Zigzagoon, Linoone, double Slash!" Willie called. Both of the opposing Pokémon jumped into the air, claws sharpened and ready to slice.

"Pikachu, Quick Attack!" Ash called in response, "Protect Muk!" Pikachu rushed forward faster than the eye could see, and was at Muk's back before either of its opponents had fallen three feet.

"Thunderbolt!" Ash yelled. Pikachu charged its electrical energy and zapped. Both of its opponents were hit and fell to the ground.

"We're not done yet!" Willie yelled, "Quick Attack, let's go!" Both Zigzagoon and Linoone charged forward at Pikachu and Muk at top speed.

"Muk, cover Pikachu!" Ash called quickly. Muk spread itself out over Pikachu as ordered, leaving the electric mouse breathing room. The two raccoon Pokémon collided with Muk's soft body and did nothing except get themselves stuck.

"Now, let Pikachu go and use Giga Drain!" Ash called. Pikachu slipped out from under Muk and Muk began to sap away the opponents energy. Both of them fell out of Muk weakly. Before Ash could call out a finishing move, Willie walked onto the battlefield. Ash, seeing that the battle was over, also walked onto the battlefield. They returned their Pokémon before speaking (Pikachu, of course, jumped onto Ash's shoulder).

"You're a great trainer Ash," said Willie as they met in the middle of the battlefield and shook hands, "I've never seen anyone battle like that! You remind me of another young man I met a couple years back…"

"Thanks," said Ash, "My goal is to become a Pokémon Master!" Willie nodded his head in approval.

"You're on the right track, I'll give it that," said Willie, "But I'll beat you the next time we battle and show you who the strong one is."

"We'll see," said Ash.

"But for now, I'd better get you out of here," said Willie as he turned back towards the Outskirt Stand, "Follow me." Ash followed Willie around the back of the Outskirt stand, where a hover bike was parked.

"I can take you as far as Drussel City, and then I'll be too far out from the Outskirt Stand," said Willie, "This place is pretty much my home. Drussel City is right on the edge of the desert, and you should be able to get a ride from there."

"Thanks Willie," said Ash.

"No problem at all," said Willie. He hopped on the front seat of the bike while Ash sat on the back and held on tight.

"Hold on!" Willie called over the roar of the starting engine. The hover bike shot forward over the sand at top speed. They were off to Drussel City.

* * *

It was only about an hour before the city came into sight. There weren't many tall buildings, but there were many buildings nonetheless. Willie pulled in right outside of it.

"Here we are!" he exclaimed, "Drussel City. One of the most overlooked places in Orre."

"So not many people come huh?" Ash asked.

"Correct," said Willie, "Still, there are plenty of people you can talk to here and someone's bound to have means of transportation." Ash got off the bike.

"Thanks for everything Willie," said Ash as Willie prepared to turn the bike back on.

"No problem Ash," said Willie, saluting, "Stay in touch." And with that he flew off into the desert, Ash and Pikachu both waving him off.

* * *

The town was rather tidy despite the run-down factor that surrounded it. People walked along the paths chatting gleefully as Ash walked down the main road. It ended at a semi-tall building that looked like a laboratory. Ash looked at the laboratory intently and then saw out of the corner of his eye another area to his right that looked like a battle arena. People were swarming around it. Ash walked towards the battlefield as well and Pikachu managed to get a view of what was going on from the top of Ash's head.

What he saw were two trainers in a double battle, with a Charmeleon and Gloom on one side, and a Tentacruel and Staravia on the other. As Pikachu watched, its ears perked up at the movements of the Gloom. It seemed to be using similar attacks to the Ledyba Ash had captured. The other three Pokémon were tiring while the Gloom itself seemed to not be losing strength at all, in spite of some of the hits it was receiving. Eventually, the Gloom defeated both of its opponents. Its trainer was declared the victor.

The crowd parted and Ash moved off to the side. The victor was being led by the judge off of the battlefield and towards the laboratory. The Gloom was still out of its Poké Ball. Pikachu jumped off of Ash's head and tried to explain things to him. Ash understood and looked up at the Gloom. He closed his eyes and let his Aura flow. Then he saw a mental image of all Aura in the area. The Gloom's Aura was a moving blob of darkness.

That caused Ash to run up to the two people walking away from the battlefield. Pikachu jumped on his shoulder again.

"Hey!" he called, "Can take a look at your Gloom?" The two people turned around.

"Who are you kid?" the judge asked. He was wearing a labcoat and opaque glasses, at least from the front.

"My name is Ash, and I'm from Pallet Town in Kanto," said Ash, "Your Gloom seemed really powerful. I really want to know what you did to it to make so strong." The Gloom's trainer smirked.

"It doesn't take a lot of work," he said smugly, "Shall we take him in and show him?" The scientist pondered the action for a few seconds.

"I guess so," he said finally, "Come with us. You can't stay for long, but we can give you a short tour of our facility." Ash followed the two men to the facility and they climbed up two sets of stairs to reach the entrance.

When the scientist pushed the doors open and led them inside, Ash looked around in amazement, shock, and absolute terror. All around there were Poké Balls running through tubes into large containers that were shaking violently. Each Poké Ball came out within five seconds looking just as it had when it went in, but the reason Ash was terrified was because within the Aura side of his mind, darkness was everywhere in the facility. He wasn't even paying attention to the words of the scientist as they walked through the facility because he was busy looking around at all of the things going on.

"That ends things," said the scientist, snapping Ash out of his trance, "You may leave now." Ash looked around again and then slowly backed away before turning and running. The scientist smirked.

"Get him," he said. The trainer nodded and ushered Gloom forward. Gloom shot forward at Ash who was halfway to the door. Out of panic, Ash threw a random Poké Ball from his belt. It was Ledyba's. Ledyba flew from the ball and collided head on with the Gloom. The scientist threw another Poké Ball and an Electabuzz came out.

"Electabuzz, use Thunder!" he yelled. An enormous bolt of pure electricity was blasted at Ash and his Pokémon.

"Pikachu, counter with Thunderbolt!" Ash yelled. Pikachu responded sending a blast of lightning straight at the Thunder attack. The attacks collided and exploded, throwing both sides back. When Ash was able to see again, both sides still were standing, albeit very bruised, especially the Shadow Pokémon. Ash made an attempt to return Ledyba to its Poké Ball.

"Ledyba, return!" Ash yelled pointing the Poké Ball at Ledyba. Ledyba dodged the beam of light deftly and turned around to face Ash snarling. The scientist and the guy both smirked.

"A Shadow Pokémon that won't listen to its trainer eh?" the scientist said, "Typical for someone who doesn't know how to control their power." Ledyba charged at Ash in a powerful shadowy aura. Pikachu stopped the attack with Iron Tail. Ledyba was knocked to the ground. Both men laughed at Ash.

"The foolish kid!" the scientist exclaimed, "Has to knock out his own Pokémon he does!"

"So kid," the other man sneered, "Still think you can beat us?" Ash gritted his teeth and glared at them for a few seconds. Then he scooped Ledyba off of the ground, and Pikachu jumped up on his shoulder and they ran. The man tried to go after him but the scientist stopped him.

"He's not for our cause," said the scientist, "But that just means that he'll find the way to purify that Shadow Pokémon eventually." The other man relaxed.

"Ah, I see what you're saying," he said, "No shadow energy means less power."

"That Pikachu is particularly impressive though," said the scientist, "Put up a lookout for him. A Pokémon like that is too good to miss."

* * *

Ash ran as far as he could into the city before stopping to catch his breath. Pikachu looked down at Ledyba worriedly.

"It's alright Pikachu," said Ash comfortingly, "You did what you had to do." On the inside he had to wonder a thought he had been wondering since the battle on the Libra, "_They called Ledyba a Shadow Pokémon… is it true?_" What he did know is that he didn't know how to handle such a Pokémon. He needed to get to the Pokémon HQ Laboratory in northern Orre quickly. Perhaps Professor Krane would know what to do.


	4. Michael

Chapter 4: Michael

"Pikachu, Thunderbolt again!" Ash yelled frantically. He paused for a moment to let Pikachu initiate its attack and delay their pursuers. Then it was off to running through the streets of Drussel City again. What had happened you might ask? Ash had been walking along the main road so as to find someplace where he could take Ledyba for healing, when he was suddenly ambushed by a group of men and women in white outfits and bandanas, similar to the two goons on the S.S. Libra. He didn't know where they had come from, but what he did know was that their number was growing, and the police were on their tail. The sirens had been blaring since five minutes into the chase.

Two more Thunderbolts ensued, and by that time, Ash was running out breath and Pikachu out of energy. Ash held the exhausted electric mouse in his arms as he ran through narrow streets and alleyways, hoping that he would find a way back to the main road. Given how far he had strayed from it however, that wasn't likely.

Finally, Ash found himself stuck in a corner. He turned into a dead end, ran to it, and turned about, looking for a way out. He found none. One of the goons stepped out of the crowd.

"Hand over the Pikachu and we won't hurt you," he said threateningly.

"Never," Ash said through gritted teeth, "You people have something to do with why my Ledyba is as hostile as it is. I'd never give Pikachu to people like you."

"I think 'hostile' is the wrong word to use," said the goon, "I would use the word 'powerful' if I were you."

"It doesn't matter how powerful a Pokémon is if they act like Ledyba does!" Ash yelled, "Then they just become monsters!"

"And how do you know that Ledyba doesn't always act that way?" the goon asked, folding his arms. Ash narrowed his eyes at the goon.

"I can see it and feel it," he said, "Something is wrong with Ledyba's Aura. It's covered in darkness." The goon stared at him through the nearly opaque black visor that covered his face.

"He's an Aura reader…" the goon whispered. At that moment, a blast of lightning shot through the crowd of goons and struck a ladder far above Ash's head. The goons were stunned momentarily as something rushed past Ash and jumped off of the walls, grabbing the ladder and extending it down the wall. Ash turned to see what had zoomed past. It was a Jolteon. As the ladder came down to the point where Ash could reach, it let go and rushed in front of Ash, fur sparking violently.

"Don't just stand there!" the goon that had been conversing with Ash yelled, "Attack!" All of the goons reached for their Poké Balls. A voice rang out before any of their hands could reach below their abdomens.

"Jolteon, use Pin Missile!" Jolteon's fur glimmered for a second and then unleashed a barrage of needles at the goons. They were delayed yet again, giving the Jolteon's commander enough time to run through the crowd and release another Pokémon. A Teddiursa appeared.

"Fury Swipes!" the trainer yelled. Ash watched gaping as the little bear Pokémon slashed its way through all of the goons as though a flash of light. The Teddiursa landed on the trainer's right shoulder and clung to it. The sirens of the police could be heard coming closer as the trainer ran up to Ash, who was still gazing in awe at his savior. This trainer wore baggy jeans held up by a belt with a pouch that Ash assumed to be where he kept his supplies. He wore a black shirt under a yellow vest that covered his whole torso. His hair was red and spiky and he wore a blue headband. His eyes were green and he couldn't have been any more than a year older than Ash.

But Ash was staring at none of that. What he was so interested in was the boy's arm. There was some sort of a machine with two parts, connected by a wire, one part that rested on his shoulder (not the one his Teddiursa held onto mind you), and the other that covered his hand like a glove.

"Come on," the trainer said, walking past Ash and over to the ladder, "We need to get out of here fast." Ash was still stunned for a moment, but then he followed the trainer (who had returned his Jolteon to its Poké Ball) holding onto Pikachu as the climbed up the ladder, just as the police were arriving below them. The trainer above Ash waved them off and one of them nodded. They continued up until they were on the roof of the building.

"Now," said the trainer as Ash pulled himself over onto the rooftop, careful to keep Pikachu away from anymore danger. The trainer spun around and looked down at Ash, who was catching his breath and cradling Pikachu in his arms.

"Any questions?" the trainer asked, flashing a smile. His Teddiursa stared at Ash intently.

"Who are you?" Ash managed. The boy crossed his arms.

"The name is Michael," he said confidently.

"And those people?" Ash asked, gesturing to the commotion below them. Michael sighed.

"They're called Cipher," he said, "They're an organization that terrorized Orre with Shadow Pokémon five years ago. They were defeated by a young man named Wes."

"But if they were defeated…" Ash started. Michael cut him off.

"They're back," he said, "And they've already done some pretty nasty things. Terrorizing people, turning Pokémon dark… all their doing. Professor Krane sent me personally to…"

"You know Professor Krane!?" Ash cried, jumping up. Pikachu had perked up as well and climbed onto his shoulder. Michael was a bit stunned now.

"Well… yes, I live at his laboratory up in the north," he said, "But anyways, he sent me to investigate Cipher's activity in this city. There was a rumor going around that there's a whole laboratory here dedicated to…"

"Making Shadow Pokémon?" Ash finished.

"How did you know?" Michael asked suspiciously. Ash explained how he had gone into the Shadow Pokémon making laboratory after noticing the shadowy aura around the Gloom that was battling on the battlefield. Michael nodded along.

"Ah, I see," he said, "I happened to be watching that battle somewhere in the crowd. I saw it too, but I didn't think of approaching the person." He tapped a small device above his ear and a scanner came out of it, moving in front of his left eye.

"With this thing I can see Shadow Pokémon," he said. Then he tapped the machine on his hand.

"And this thing… it allows me to capture them," he continued.

"You mean they can't be captured by normal Poké Balls?" Ash asked.

"It's not that," said Michael, shaking his head, "Wild Pokémon have a hard time surviving in Orre. The weather is too severe. Even Shadow Pokémon can't take it. So most Pokémon in the region are under the care of trainers. Unfortunately, that care that Shadow Pokémon are under…" Michael trailed off and Ash nodded, thankful that he had caught Ledyba before it could go to far.

"But anyways," said Michael, "I have a question for you: how did you see that Gloom's Aura without an Aura Reader?" Ash took a deep breath.

"A while back I found out that my Aura is perfectly in sync with that of the world around me," said Ash, "It's like a sixth sense. I never use it though, because I've only ever needed it in dire situations." Michael stared at Ash.

"You're a living Aura Reader…" he said with a sense of disbelief. He looked to the sky.

"I'm taking you to the HQ Lab," said Michael, "You need to see Professor Krane."


	5. Aura, Aura, Everywhere

Chapter 5: Aura, Aura, Everywhere

It turned out Michael had a bike too, but this one didn't hover. Ash though about bringing up Willie's hover bike to him, but he decided against it and just went with the flow. According to Michael, they were going to make a stop in Agate City to check on something. They pulled into the city, a small quaint place built into the nature around it, about an hour after leaving Drussel City.

"It's sort of a retirement village," said Michael, "A lot of old folks living around here." Ash nodded. He hadn't said much to Michael, other than his name, so the other trainer didn't know anything about where he had come from, or about his Ledyba. "_Ledyba…_" he thought. He suddenly realized that he had never taken his Pokémon to a Pokémon Center in Drussel City.

"Is there a Pokémon Center here?" Ash asked, somewhat frantically. Michael nodded. Ash caught his breath and breathed out. Michael pointed him towards it and they parted ways for the time being.

* * *

The bell dinged for Ash to come pick up his Pokémon. He got up from the table he had been sitting at and went to the counter. Pikachu immediately jumped on his shoulder, fully refreshed. He took the other two Poké Balls from the tray and attached them to his belt. He bowed to the nurse and went back to his table, examining Ledyba's Poké Ball.

It was strange to him. It was as if his Aura senses were opening up. While nobody knew it, he had started to have short, uncontrollable bouts of seeing the Auras around him after he had used the ability to see the Gloom's Aura in Drussel City. And every time that happened, Ledyba's was the darkest. He couldn't even see through the dark fog that surrounded the little bug Pokémon. It pained him, because he couldn't connect with Ledyba through that shroud of darkness at all.

Another bout of Aura sight occurred. He saw the foggy blue Auras of the people and Pokémon around him. All of the Aura in the room was blue while everything around the blue was colored in negative. He looked down at Ledyba's Poké Ball slowly. It was still shrouded in darkness. He held the Poké Ball close to his face and shut his eyes.

"_There must be a way through to you…_" Ash's thoughts echoed through the Aura vision, "_You must have a way to open up…_" He gripped the ball tighter and focused ever harder. He started to gain control over the vision. Then a voice cut through it.

"Ash!" Ash's concentration broke and he gripped his head as he sprawled out across the table. Michael ran up to him.

"Ash, are you alright!?" Michael cried, "You looked as though you were about to explode!" Ash opened his eyes and looked around slowly. Pikachu was sitting on the table now, gazing at him worriedly. Ledyba's Poké Ball had rolled onto the table and was sitting there silently.

"What were you doing?" Michael asked. Ash grabbed Ledyba's Poké Ball off of the table. Oddly enough, it didn't shake in protest. Then he stood up.

"Just thinking," he said. Michael nodded.

"Well, there's someone I want you to meet," said Michael, "He knows a lot about the Shadow Pokémon incident." Ash stood up from the table and nodded. Michael then led him out of the Pokémon Center.

They happened to run smack into the person Michael wanted Ash to meet. Or rather he ran smack into them. As they walked up a grassy slope, a man in purple robes and white hair hanging down to his back, eyes that were nearly shut from wrinkles, and a long white beard, came running down the slope, slamming into them and sending them toppling back down to the bottom.

Immediately, the man was down by them, helping them up.

"I'm so sorry boys!" he cried, "I was in such a hurry…"

"We understand, Eagun," said Michael, "You're always in a hurry."

"Ah, there you are Michael," said Eagun, dusting off Michael's shirt, "Now where is this other person you wanted me to meet?"

"Right in front of you," said Michael, "Eagun, this is Ash." Eagun forcefully shook Ash's hand.

"Nice to meet you Ash," the old man said. Ash nodded absently. What the other two couldn't see was that he was in another Aura vision. Everything around him moved slowly. Words reverberated through the air in echoes. The blue Auras of the people of Agate swirled around him, and his head hurt from all that he was taking in. As he observed this, his hand clutched Ledyba's Poké Ball at his belt. The more he held onto it, the more welcoming its grip felt to him, as if Ledyba itself was opening to him.

"Ah, so he is an Aura seer!" Eagun exclaimed. The words broke Ash out of his trance.

"Yes, he is," said Michael, "He can see the dark Auras around Shadow Pokémon and any other Auras around him." Eagun rubbed his chin.

"Yes, yes…" he said, "And what about purification abilities?" Michael seemed taken aback.

"Purification… abilities?" Michael asked, "What do you mean?" A sound beeped from Michael's belt. Michael pulled a small device off of it and flipped it open.

"What's that?" Ash asked.

"My PDA," said Michael, pressing a button. After a few moments, his face scrunched up.

"That's strange…" he said, "I don't remember catching a Shadow Ledyba." Ash perked up.

"Strange indeed," said Eagun, "That Shadow Monitor was made to monitor Shadow Pokémon that have been caught and their progress to purification was it not?" Michael nodded.

"But I thought it was limited only to me," he said. Ash, having no clue what they were talking about, spoke up.

"Uh… I think I might have a Shadow Ledyba," said Ash. The other two turned to him in surprise.

"Where did you get it?" Michael questioned, "Let me see it." Ash reluctantly reached for Ledyba's Poké Ball. As he raised it to call Ledyba out, another Aura vision overtook him. This one split through his head for a few seconds, but when he was able to see clearly, he saw that Ledyba had been called out. The darkness of its aura had receded to a small amount right at its center.

"It's… ready to be purified!" Michael exclaimed. The words echoed through Ash's head and the vision ended. It turned out that he had almost fallen over, but Eagun had caught him. As Ash regained his balance, Michael asked him:

"How long have you had this Ledyba?"

"Since this morning as far as I know," said Ash. Michael looked between Ledyba, who was staring off into space blankly, and Ash in confusion.

"Well, it seems that I was right," Eagun mused, "The boy must have purification abilities."

"I've never heard of such a thing as someone being able to purify Pokémon on their own power," Michael objected.

"You use the Cologne Case on occasion do you not?" Eagun countered, "All of those scents are in tune with different Aura wavelengths. The Vivid Scent is the strongest of them, the one in tune with the strongest Aura wavelength that we know of. But Ash here… I believe that the wavelength of his Aura is perfectly even, giving him the ability to not only see Auras, but manipulate them as well." Michael stared at Ash, a look of denial tinting his eyes. Ash finally decided to speak up.

"Can someone please explain what we're talking about here?" he asked pleadingly, "Shadow Monitor? Purification? Cologne Case?"

"That's an explanation for another time," said Eagun, "Right now, we need to get this Ledyba to the Relic Stone." Michael's look of doubt receded, albeit slowly.

"Right," he said, "Ash, return Ledyba to its Poké Ball and follow us." Eagun rushed off the second those words were said. Michael rolled his eyes and quickly walked after him. Ash, still confused, returned Ledyba to its Poké Ball and rushed after them.

* * *

Ash found the two of them at the end of a cavernous tunnel beneath the town. Eagun rushed out of it and Michael gestured for Ash to follow. Ash did so.

The clearing he walked into was incredible. All around, forest bloomed. There was almost nothing but green for miles in every direction. Ash and Pikachu were awed at the sight.

"Now normally I would have to battle you to determine your worthiness, but your abilities say enough about you to me," said Eagun, "You are worthy of using the Relic Stone." Ash hesitated.

"Go on," said Eagun. Ash drew Ledyba's Poké Ball from his belt and approached the Relic Stone, a cylindrical stone jutting out of the stone ground underneath his feet. It was offset in a few different places, but it stood firm on the rocks. As Ash approached the stone, Ledyba's Poké Ball began to flash in a soft green light, as did the offset areas of the stone. Michael watched him curiously as he brought the ball within contact of the Relic Stone.

Ledyba automatically popped out and a green light surrounded it. Ash was absorbed into another Aura vision. He saw Ledyba's Aura shift violently between dark and light. Finally, the darkness left Ledyba and was taken over by the light. The dark Aura vanished and the green light around Ledyba faded to blue within the vision. Ash could see Ledyba clearly.

The vision ended and Ash blinked. Ledyba looked confused still. The bug Pokémon's eyes shifted around until they settled on Ash. She gently hovered towards him with sad eyes and looked up at him. Ash smiled and held out her Poké Ball in his hand. She smiled as widely as a Ledyba could smile and put herself within the ball. Ash gripped the ball tightly in his hand.

"Welcome to the team Ledyba," he said.

* * *

**A/N: Sorry for a being a while in updating. I kept second-guessing myself with this chapter. That aside, I will say this: that I have called someone by the wrong name in this story. I've fixed all of the errors. I still can't believe that I've been calling Rider Willie by Vander's name for about a year now. **

**While I'm here, I'll say I do not own Pokémon, all of it belongs to Gamefreak and Nintendo. **


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